Direct Docker Usage¶

In [1]:

# Galaxy settings
GALAXY_SERVER=${GALAXY_URL}
GALAXY_API_KEY=${GALAXY_API_KEY}

# set the working dir: path must be absolute as Docker requirement
WORKSPACE="$(pwd)/.." #${WORKSPACE:-$(pwd)}

# absolute path of your test definition and test data
LOCAL_INPUT_FOLDER="${WORKSPACE}/examples/change_case"
LOCAL_OUTPUT_FOLDER="${WORKSPACE}/results"

# test definition file relative the $LOCAL_INPUT_FOLDER
TEST_DEFINITION_FILENAME="workflow-test.yml"

# test to be executed
TESTS="change_case"

# Docker settings
DOCKER_IMAGE="crs4/wft4galaxy"
DOCKER_INPUT_FOLDER="/data_input"
DOCKER_OUTPUT_FOLDER="/data_output"
DOCKER_CONFIG_FILE="${DOCKER_INPUT_FOLDER}/${TEST_DEFINITION_FILENAME}"

# run test
docker run -i --rm \
              -v "${LOCAL_INPUT_FOLDER}":${DOCKER_INPUT_FOLDER} \
              -v "${LOCAL_OUTPUT_FOLDER}":${DOCKER_OUTPUT_FOLDER} \
              ${DOCKER_IMAGE} \
              --server ${GALAXY_SERVER} --api-key ${GALAXY_API_KEY} \
              -f ${DOCKER_CONFIG_FILE} \
              -o ${DOCKER_OUTPUT_FOLDER} ${TESTS}

2016-11-12 13:25:18,992 INFO: Configuration: {'galaxy_url': None, 'enable_logger': True, 'galaxy_api_key': None, 'enable_debug': False, 'disable_cleanup': False, 'output_folder': '/data_output', 'workflows': {'change_case': WorkflowTestConfig: name=change_case, file=workflow.ga, inputs=[InputText], expected_outputs=[OutputText]}, 'disable_assertions': False, 'logger_level': 20}
Workflow Test: 'change_case' ... 2016-11-12 13:25:19,721 INFO: Create a history '_WorkflowTestHistory_74db7ef5-a8db-11e6-96ae-0242ac110002' (id: u'8f9e5986e31a6d36')
2016-11-12 13:25:21,666 INFO: Workflow '_WorkflowTest_Change Case (imported from API)' (id: 6d2d4099ead26222) running ...
2016-11-12 13:25:29,477 INFO: Workflow '_WorkflowTest_Change Case (imported from API)' (id: 6d2d4099ead26222) executed
2016-11-12 13:25:29,482 INFO: Checking test output: ...
2016-11-12 13:25:29,623 INFO: Checking test output: DONE
ok

----------------------------------------------------------------------
Ran 1 test in 11.003s

OK